Hi, I would like to place "\n" after every sequence in a FASTA file. My FASTA file looks like this:
>pdb|5U15|L Chain L, Crystal Structure Of Dh270.uca3 (unliganded) From The Dh270 Broadly Neutralizing N332-glycan Dependent Lineage
QSALTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGKAPKLMIYEVSKRPSGVSNRFSGSKSG
NTASLTISGLQAEDEADYYCCSYAGSSTVIFGGGTKLTVLGQPKGAPSVTLFPPSSEELQANKATLVCLI
SDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTV
APTECS
>pdb|5U15|H Chain H, Crystal Structure Of Dh270.uca3 (unliganded) From The Dh270 Broadly Neutralizing N332-glycan Dependent Lineage
QVQLVQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGWINPNSGGTNYAQKFQGRVTM
TRDTSISTAYMELSRLRSDDTAVYYCARGGWISLYYDSSGYPNFDYWGQGTLVTVSGASTKGPSVFPLAP
SSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYIC
NVNHKPSNTKVDKRVEPKSCDKHHHHHH
I would like to modify the file as:
>pdb|5U15|L Chain L, Crystal Structure Of Dh270.uca3 (unliganded) From The Dh270 Broadly Neutralizing N332-glycan Dependent Lineage
QSALTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGKAPKLMIYEVSKRPSGVSNRFSGSKSG
NTASLTISGLQAEDEADYYCCSYAGSSTVIFGGGTKLTVLGQPKGAPSVTLFPPSSEELQANKATLVCLI
SDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTV
APTECS
>pdb|5U15|H Chain H, Crystal Structure Of Dh270.uca3 (unliganded) From The Dh270 Broadly Neutralizing N332-glycan Dependent Lineage
QVQLVQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGWINPNSGGTNYAQKFQGRVTM
TRDTSISTAYMELSRLRSDDTAVYYCARGGWISLYYDSSGYPNFDYWGQGTLVTVSGASTKGPSVFPLAP
SSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYIC
NVNHKPSNTKVDKRVEPKSCDKHHHHHH
I have encountered a post regarding linearizing the fasta file but couldnt figure it out.
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AsoInfo
3 answers
A very simple solution would be:
cat file.fasta | sed 's/>/\n>/g' | tail -n+2
It'll add an empty line at the start of the file as well though, but I don't know if thats a problem for you. Linearising the fasta and appending to the end of the sequence line would be a more robust way to do it 'properly'
Edit: use of tail removes the leading blank line.
a short python script like the following may work for you
for lines in f:
if lines[0]=='>':
print lines
else:
lines=lines+'\n'
print lines
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nepgorkhey
As i know that prinseq is use for triming and filtering data but Can we use Prinseq tool for conversion of BAM file to FASTA format?
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Title of this post does not appear to match the request in the main body of the post. If you just want to add a gi_ before pdb you could use
sed 's/^>pdb/\>gi\_pdb/g' your_file > new_file.I have just edited the post. "gi" was added mistakingly.